[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2017-11-07T17:48:28Z"
 content="""
There have been several bug reports with that same error message
and different causes (permissions problems; filesystems on which sqlite
doesn't work etc). So all that I know from the error is something went
wrong with the sqlite database, which causes queries of it to fail.

Using the linux version of git-annex on Winows via the (misleadingly named)
"bash for windows" is pretty unusual. I have never seen it work; Microsoft
were still adding missing linux system calls to their emulation layer the
last time I tried it. It's quite possible that there remains a bug in that
emulation layer, that prevents sqlite from working, or makes it unreliable,
etc. I cannot reproduce the problem running git-annex on Linux.

Note that since it's a v6 repository, running `git add` actually adds the
files to git-annex. `git add` unfortunately runs `git-annex smudge` once
per file. As you note, this is slow; this is one of the several reasons
documented in [[todo/smudge]] why v6 mode is still considered experimental;
and it will need changes in git to improve the speed).

It would be useful to know if it's failing on the first file, 
or if several files get processed ok before it begins to fail.
You could set `GIT_TRACE=1` in the environment to find out.
"""]]